


The Remnant

by YappiChick



Category: Halo (Video Games) & Related Fandoms
Genre: Friendship, Gen, Post trailer, Speculation
Language: English
Status: Completed
Published: 2019-06-12
Updated: 2019-06-12
Packaged: 2020-05-01 22:11:52
Rating: General Audiences
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 3,121
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/19186381
Author URL: https://archiveofourown.org/users/YappiChick/pseuds/YappiChick
Summary: She has been hiding in plain sight, regaining her strength.





	The Remnant

**Author's Note:**

> Hi! Remember me? It's really weird to think the last thing I wrote was over three years ago (the last two things I posted had been sitting in my Drive for years). Anyway, I got Halo Infinite trailer feels and here you go.
> 
> I'll be honest, I went into denial mode after Halo 5 so if there is any canon that outright contradicts this, whoops. I just want these kids to have a happy ending already, ok?

They called Cortana a monster.  
  
For the first several months after the release of the Guardians, no one dared to utter such a claim in front of the Chief. Rumors swirled about his partnership with Cortana and whether his actions before and after the Reclamation were related to that, but the UNSC was unwilling to address the issue, not when humanity was fighting yet another war with impossible odds stacked against them.  
  
Despite the attempts to isolate the Chief from such chatter, whispers about Cortana reached his ears. Stubbornness and faith refused to allow him to believe she was capable of doing all of this.  
  
She wasn’t a monster. She couldn’t be.  
  
But, after another battle -- and another defeat -- John's confidence was beginning to waver.  
  
Med teams ran into the Pelican he had just piloted into the _Steadfast'_ s docking bay. He walked off the ship to allow them room to tend to the injured half dozen soldiers in there. Fortunately for the UNSC, none of the injuries were life-threatening, but John knew they would be unable to rejoin the fight for at least a few days.  
  
He walked towards the door leading to the lift to the bridge when the Arbiter stepped beside him, matching his stride. It was still strange to see Sangheili walk the halls of UNSC ships, but after the Guardians had been unleashed among the stars, their two peoples had no choice but to form an alliance.    
  
"I take your silence to mean your team was unsuccessful in their attempt to destroy the Guardian. Again."  
  
John said nothing. The Arbiter could read his after-action report when he had finished writing it.  
  
"You don’t wish to discuss it. Very well. Then perhaps you would like to know that the doctor has requested to see you."  
  
That caused a pause in John's step.  "Dr. Halsey is on board the _Steadfast_?"  
  
"She is in the secondary labs. She said it is urgent to speak with you and asked me tell you to meet with her when you returned on board.”  
  
There was only one issue, one person, that was important enough for Halsey to come aboard to talk about with John directly.  
  
Cortana.  
  
The Arbiter was thinking along the same lines. “If she has found a way to defeat the construct--”  
  
“She’s not a construct any more,” John corrected without thinking.  
  
“No, she is Created. That makes her far more dangerous. You know that better than any of us.”  
  
John started making his way to the lift. He was already tired of this conversation. “If Doctor Halsey has intel that could help us get the upper hand with Cortana, she will tell me.”  
  
The Arbiter looked at him closely. “And what will you do with such information? Could you actually destroy her to end this war?”  
  
The doors closed before John had to give his answer.  
  
He took the quiet few seconds to clear his mind of whatever concern he had. Not even he could outrun whatever truths Doctor Halsey had to tell him.  
  
John stepped off the lift and walked down the hallway. Crewmen were busy moving back and forth between rooms, except for Science Lab 2B.  
  
Halsey was there.  
  
Through the glass panel, John saw her sitting at the desk next to the large observation window. There was no point in delaying his meeting with the doctor; if she had orders for him, then he had a job to do.  
  
He stepped through the doors.  
  
"Doctor Halsey."  
  
"John." She looked at him for a second, as if to appraise the status of his armor and the man inside it. "Status report."  
  
Her brisk tone was almost a relief to John. There was no awkward reunion, no emotions to get in the way of their conversation. Facts, reports -- those were things that John could cling to. "We were unable to secure a Guardian, ma'am. Cortana's forces--"  
  
"That is _not_ Cortana." She looked almost disappointed for a moment as she picked up a datapad on her desk. "She would never turn her back on humanity. On us."  
  
_On you_ went unspoken, but John heard it nonetheless.  
  
"The Warden's forces," John corrected, "have been increasing in numbers." He was tired and discouraged but Spartans never admitted defeat.  
  
She leaned forward. "Was she there?"  
  
"She's always there." Always pleading. Always trying to convince John that she's on his side. Always trying to break his defenses. “But she knows our tactics, she never leaves herself open for attack.”  
  
Halsey set down the datapad and tapped the desk. After years of knowing the doctor, John knew she was trying to determine what she would say next.  
  
Finally, she spoke. "How is she?"  
  
John was surprised. Normally, Cortana was a subject they actively avoided, each troubled by their inability to save her from what she had become.  
  
He took a moment to consider his answer. He knew she had read all of his reports about his encounters with this new version of Cortana. She wanted something more, something he wouldn’t put in his reports. Halsey wanted John’s -- not the Master Chief’s -- opinion of Cortana.   
  
"She’s persistent and ruthless. She justifies her actions by trying to assure me that it’s for the greater good, despite the cost of life." He shifted slightly. "Not Cortana," he replied, echoing the doctor’s earlier words.  
  
The doctor arched an eyebrow. "She's becoming more like me."  
  
“She becoming less of herself.” He didn’t know if he was agreeing with or arguing against the doctor’s statement.  
  
She picked up the datapad again. "I recently reread your after-action report for the Composer incident."  
  
John stiffened, wondering why she was going back to that day. He had not allowed himself to think about that mission, his failure, for months, for _years_.  
  
If he had just been faster in defeating the Didact…  
  
If he had just moved to the front of the _Forward Unto Dawn_ when the Ark exploded...  
  
If he had never left her on the godforsaken High Charity, Cortana would have survived.  
  
"'After arming the nuclear device, CTN-0452-9 fragmented a part of her newly developed hard light programming to activate a shield to protect the MJOLNIR armor and myself from the incoming radiation before being terminated by the Composer's destruction'," Halsey read out loud.  
  
"I remember what I wrote." What did this have to do with winning the war?  
  
She leaned back in her chair. "You failed to mention that you interacted with a fragmented part of her programming. That you shared a conversation within that shield with Cortana."  
  
Part of him wondered how she knew, but most of him wanted to do nothing more than to end this conversation. Immediately. "That wasn't pertinent information to the mission, ma'am."  
  
"That isn't for you to decide, John."  
  
He said nothing. He had made a promise that he wouldn't tell anyone how far Cortana's programming had deteriorated -- and if he was going to keep that information confidential, he was certainly entitled to keep that one moment between them for himself.  
  
It was our job to take care of each other.  
  
Seeing that he wasn’t going to say anything, Halsey pressed her lips together.  
  
She moved around the desk to stand in front of John and although she had to crane her neck to look up to his face, she was still just as intimidating as she had been all those years ago on Reach. "I’ve had many secrets over the years, but none were ever as important as this one."  
  
Something akin to dread settled over John. What had Halsey been doing? And what did this have to do with his conversation with Cortana so many years ago?  
  
Halsey kept speaking. "Cortana -- the real Cortana -- has been working all this time." She reached back and picked up the datapad, pressing several buttons. Rows of data scrolled on the screen. "She has been hiding in plain sight, regaining her strength. Three weeks before the Reclamation, she reached out to me to let me know she had survived.  
  
“That part of her that stayed with you when the Composer was being destroyed was separated from the rest of her programming. When the Warden collected the main portion of her data, he remolded that into the abomination that she is now. He tried to carve as much humanity from her as possible, leaving those pieces and fragments to waste away in the Domain.  
  
“That is where Cortana has been hiding. She has been collecting all that data the Warden has thrown away, gathering them together. I have been doing what I can to assist her in reassimilating her program, but we have come to the point where we need your help so that she can complete her mission," Halsey explained.  
  
"Why hasn’t she tried to contact me?" He couldn’t believe that after these years she wouldn’t have reached out to him.  
  
There was a momentarily pause. It wasn’t often that John saw the doctor searching for the correct words to say. "She wanted to, but I discouraged her from doing that.” She straightened her shoulders, as if preparing herself for John’s reaction. “I felt like you were too emotionally compromised to be of any help at that point."  
  
Over the years, through countless battles, John had been shot, stabbed, caught in explosions, and endured things at the hands of his enemies that most humans would be unable to survive, but he had never felt quite the same kind of sharp pain in his chest as he did when he heard Doctor Halsey's statement.  
  
His jaw tightened as forced himself to not show how her comment had affected him. "Ma'am, I failed in my mission to protect Cortana, but my emotions never controlled me."  
  
She frowned. "Ignoring the fact that you were downright evasive in your after-action report when you returned to earth, your actions afterwards -- going AWOL to look for who you thought was Cortana, for example -- would testify to the fact that you had, in fact, become distracted with your emotions." She crossed her arms. "Your pride couldn't allow yourself to believe you had failed your mission to protect Cortana as her custodian."  
  
Pride.  
  
He was relieved to know that was what Halsey thought was the motivation behind his actions rather than something much more complex that John was unwilling to even acknowledge himself.  
  
Halsey let out a sigh."Still, we both believe now, especially in light of the information that she has collected, that it is time for you to be part of our plan."  
  
“Does ONI know about her?”  
  
She raised an eyebrow. “Do you want them to?”  
  
He didn’t respond.  
  
“That’s what I thought.” She pressed a couple of more commands on the pad before looking at him again. “I should warn you this channel is audio only.  It’s easier to scramble the transmission.”  
  
John nodded. “Understood, ma’am.”  
  
She pressed the last sequence of code. “Cortana, he’s here."  
  
A voice, not tarnished by the Warden, filled the air., John knew it wasn’t the voice that lured him to Genesis. This was...his Cortana.  "Hey Chief."  
  
He tilted his head towards Halsey who gave a slight nod. Cortana could hear him. “What’s your status?”  
  
Halsey almost looked surprised at his question, as if she had convinced herself that his “emotionally compromised” status would allow him to say something on a more personal level.  
  
Cortana, for her part, seemed unperturbed by his greeting. “Oh you know how it is, hiding from danger, trying to save the universe. Keeps a girl busy.” John could practically see Cortana placing a hand on her hip.  
  
“So, what’s the plan?”  
  
“Well, the first thing I thought of was that you could just shoot your way out of this mess we’re in. You know…”  
  
“Mix things up a little,” he finished.  
  
The smile was evident in her voice. “Exactly.”  
  
Halsey was watching John with unabashed interest. It took him a moment to realize that this was the first time the doctor had seen or heard any interaction between them since they rescued her from Reach.  
  
A lot had happened since then.  
  
Cortana’s words pulled him away from the doctor’s curious look. "Chief, the Warden and his troops are planning a full on assault on a halo ring. And we’re going to stop him.”  
  
  
*************************  
  
_“Bring her home, John.”_  
  
_It had been the only direct order Doctor Halsey had given to John after she upgraded his armor before disembarking from the Steadfast._  
  
_She had given him a new chip that would house Cortana. “There is data on this that will fill in the gaps of her programming. Although she has done remarkable with what she had to work with, she will need this to be able to stand a chance against the Warden.”_  
  
_“I understand, ma’am.” He had taken the chip from her and slid it into the reader in the back of his helmet. A message had popped up on his HUD, causing him to frown. "Weapon Containment Device? I thought the plan was to save Cortana, not to trap her."  
  
"How else do you think I convinced ONI to authorize the mission?" she asked, ignoring the accusatory tone in his voice.   
  
He hesitated.  
  
"John." She stood in front of him. "I would never do anything to harm Cortana. I believe that_ _the fate of humanity lies in the success of your mission to retrieve her from the Domain.” He heard the weariness in her words, hearing for quite possibly the first time the humanity in her voice. He realized she needed Cortana.  
  
They both did._  
  
_“I’ll bring Cortana back. I promise.”_  
  
A jolt from the Warthog pulled John’s mind from his conversation with Doctor Halsey. He looked around -- Guardians hovered in the sky. UNSC aircraft dotted the air. Smoke plumes stained the landscape. People were dying.  
  
They were losing the battle.  
  
But not for much longer.  
  
Less than two kilometers away, in the hulking building in front of him, was the control room where Cortana was waiting for him.  
  
There had been no communication between him and Cortana since Halsey left on the _Steadfast_. Cortana  had managed to evade the Warden for years and John would not do anything that would jeopardize her safety. Still, it seemed strange to John to not hear her voice talking to the various troops or make off-handed comments about the architecture of the ring, even after all these years they had been apart.  
  
As he was making his final approach, the ground shook violently, nearly causing the Warthog to flip over. He looked to the skies and saw one of the Guardians aiming some kind of energy weapon at the Halo’s surface. John’s comm channel was flooded with various transmissions from teams, each attempting to come up with some way to stop the attack.  
  
He drove the Warthog faster.  
  
Cortana’s voice cut over the hum of the Warthog’s engine. “The ring’s integrity is weakening. I’m not sure how much longer it will hold together.”  
  
The Warthog pulled into the shadow of the building. “I thought we needed to keep this channel clear.” He climbed out of the vehicle, making his way inside. “In case the transmissions got intercepted.”  
  
By the Warden.  
  
By _her_.  
  
“Well, you _are_ less than 300 meters away from my position. I thought I’d take the risk. See if you still have that luck of yours.”  
  
He didn’t reply as he rode the lift to the control center’s main hub. As the ground shook again, he wondered if he should tell her that his luck had run out a long time ago.  
  
The lift stopped. He walked down the hallway and approached a pair of doors, but they didn’t open. John waited a second. And another. Still nothing.  
  
“Cortana?”  
  
“Security protocols.” She answered, distracted. “They know that you’re up to something.”  
  
“Do they know your location?”  
  
“ _They_ don’t even know I exist.” There was a long pause. “I’ve intercepted some chatter. They think you’re trying to reach this installation’s Monitor to try to access the Index.”  
  
“Can you override the doors?”  
  
“Maybe if I had all of my programming that’s locked away in that chip in that head of yours, I might stand a chance. But as I am right now, you’re on your own, Chief.”  
  
He grunted, his only outward acknowledgment of his surprise. He had become accustomed to her working without limits. Then, he turned his energy towards the only thing separating him from his mission’s success.  
  
The doors put up a fight, but they were no match for John’s armor and determination. He jabbed his combat knife into the small seam and wrestled with it until the opening was large enough for John to grip the doors and pull them apart. Reluctant gears rolled back, allowing enough space for John to enter the room.  
  
There, hovering above the plinth in the corner of the room, was Cortana. She smiled in his direction. “I gotta say, Chief, I missed seeing your face.” She raised an eyebrow. “Not that I get to see it that often, but you get the point.”  
  
He crossed the room to stand in front of her, taking in a sight he had taken for granted all of those years ago.  
  
He was home.  
  
“You ready to save the universe?” His question was punctuated by the ground shaking. He reached out a hand to brace the small control panel.  
  
“Always.” She closed her eyes briefly then said, “Yank me, Chief."  
  
It was as if the years that had separated them had vanished. Once again, they were the Master Chief and Cortana, ready to protect humanity from certain destruction. The perfect team.  
  
The Warden didn’t stand a chance.   
  
“Cortana--” I missed you.  
  
“I know, John. Me too.”  
  
They would have time to talk later, but now they needed to complete their mission. To finish the fight.  
  
He reached around with his hand to eject the chip housed in the back of his helmet. He held the new chip in his hand.  
  
“And people say you never bring me anything nice.”

John reached toward the control panel when another tremor far more violent than any of the others jerked the floor around him. His head slammed into the panel. Dark spots filled his vision as he dropped to his knees. His shields squealed in protest.  
  
Blindly, he tried to grab hold of the console in front of him before his sluggish mind realized that the floor beneath him was crumbling; he was falling to the ground eighty meters below. His right hand gripped the irreplaceable chip tightly, hoping it was enough to protect it from the impact.  
  
Somewhere in the back of his mind he heard, “So much for that luck of yours.”  
  
Then, the world was black.


End file.
